Elfin UI: A Graphical Interface for Protein Design With Modular Building Blocks

Abstract

Molecular models have enabled understanding of biological structures and functions and allowed design of novel macro-molecules. Graphical user interfaces (GUIs) in molecular modeling are generally focused on atomic representations, but, especially for proteins, do not usually address designs of complex and large architectures, from nanometers to microns. Therefore, we have developed Elfin UI as a Blender add-on for the interactive design of large protein architectures with custom shapes. Elfin UI relies on compatible building blocks to design single-and multiple-chain protein structures. The software can be used: (1) as an interactive environment to explore building blocks combinations; and (2) as a computer aided design (CAD) tool to define target shapes that guide automated design. Elfin UI allows users to rapidly build new protein shapes, without the need to focus on amino acid sequence, and aims to make design of proteins and protein-based materials intuitive and accessible to researchers and members of the general public with limited expertise in protein engineering.

Template-Assisted Assembly of Hybrid DNA/RNA Nanostructures Using Branched Oligodeoxy- and Oligoribonucleotides

“…The free, open-source software Blender (version 2.82 was used in this work) [51] was widely employed for a variety of 3D modeling and visualization tasks in molecular biology, e.g., for visualization of antibodies [52], for protein design [53], for a 3D representation of a DNA origami receptor [54], and for modeling of amyloid fibrils [55]. Using Blender, relatively simple yet informative models of DNA tetrahedron and DNA cube were previously obtained with the selected parameters [47], followed by a more complex model of a C24 fullerene-like DNA shell in the current work (Figure 3).…”

Repeat proteins: designing new shapes and functions for solenoid folds

“…Elfin [21] and its graphical user interface Elfin UI [22] have been developed for the design of protein architectures using existing building blocks with known interfaces. Repeat protein units and helical junctions can be combined directly, if interfaces are compatible (e.g.…”

A Generative Model for Creating Path Delineated Helical Proteins

“…Many recent papers that claim functional de novo designed proteins utilize helical proteins with short loops [16][17][18][19][20][21][22][23] . Repeated helical proteins are also often used as a base to iterate on larger structural architectures [24][25][26][27] . The generation of these helical backbones is commonly done by randomly or parametrically assembling sets of structural fragments [28][29][30][31] .…”